Genome-wide detection of copy number variations (CNVs) in Afghan Baluchi sheep breed using Ovine ۵۰k SNPChip array Abstract

Background and Aim: The aim of the present study was to identify copy number variations (CNV) at the genome level, in one of the main sheep breeds reared in Afghanistan named Baluchi breed, and to study the associations between these regions of interest with different biological pathways.Methods: Animal samples were collected from their natural rearing environment in Afghanistan and then were genotyped using Illumina Ovine ۵۰kSNP array. After various stages of quality control of data, the genome-wide detection of CNVs was carried out using Hidden Markov Model in PennCNV (version ۱.۰.۳) software.Results: The results revealed that all animals used in this study showed copy number variations in their genome. In total, ۶۲ CNVs were observed for autosomal chromosomes. The total genomic length of CNVs was ۹ Mbp and the average CNV numbers per animal was ۴.۱۳. After merging overlapped regions, a total of ۵۰ CNVR regions were identified. These genomic regions were then further evaluated using bioinformatics tools for identifying the metabolic pathways associated with them. After identifying the genes reported in these genomic regions and performing the gene ontology study, the results revealed that many of these regions are associated with different metabolic pathways such as fertility and reproduction performance, immune system development, and skeletal-muscular system.Conclusion: Overall, this study in Afghan sheep breeds can provide a valuable source of information to identify genomic regions associated with economically important traits in Afghan sheep breeds.

Keywords:

Afghan sheep , Copy Number Variation (CNV) , Gene ontology analysis , Genetic variation , Genomic evaluation